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.travis.yml
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.travis.yml
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sudo: required
os: linux
matrix:
include:
- language: python
python: 3.6
install:
- sudo apt-get install liblzo2-dev
- sudo apt-get install zlib1g-dev
- pip install numpy --upgrade
- pip install .
script:
- remap-gff3.py -a example_file/alignment.gff3 -t_fa example_file/target.fa -q_fa
example_file/query.fa -dir output -tmp_ID -g example_file/example1.gff3 example_file/example2.gff3 -s NCBI -b Hazt_2.0
- gff_to_chain.py -t_fa example_file/target.fa -q_fa example_file/query.fa -a
example_file/alignment.gff3 -o chain.txt
- agp_to_chain.py -t_fa example_file/target.fa -q_fa example_file/query.fa -a
example_file/example.agp -o chain.txt
- re_construct_gff3_features.py -old_g example_file/example1.gff3 -new_g example_file/example1_CrossMap_filtered.gff3
-og example1_re_construct.gff3 -re report.txt
- get_remove_feature.py -old_g example_file/example1.gff3 -new_g example_file/example1_updated.gff3
-og example1_removed.gff3
env: version=native
- language: generic
services:
- docker
install:
- docker build -t remap-gff3 .
script:
- docker run remap-gff3 remap-gff3.py -a example_file/alignment.gff3 -t_fa
example_file/target.fa -q_fa example_file/query.fa -dir output -tmp_ID -g example_file/example1.gff3
example_file/example2.gff3 -s NCBI -b Hazt_2.0
- docker run remap-gff3 gff_to_chain.py -t_fa example_file/target.fa -q_fa
example_file/query.fa -a example_file/alignment.gff3 -o chain.txt
- docker run remap-gff3 agp_to_chain.py -t_fa example_file/target.fa -q_fa
example_file/query.fa -a example_file/example.agp -o chain.txt
- docker run remap-gff3 re_construct_gff3_features.py -old_g example_file/example1.gff3
-new_g example_file/example1_CrossMap_filtered.gff3 -og example1_re_construct.gff3
-re report.txt
- docker run remap-gff3 get_remove_feature.py -old_g example_file/example1.gff3
-new_g example_file/example1_updated.gff3 -og example1_removed.gff3
env: version=docker
deploy:
provider: script
script: bash docker_push.sh
on:
branch:
- master
- add_travis
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